Format

Send to:

Choose Destination

VCX3A variable charge X-linked 3A [ Homo sapiens (human) ]

Gene ID: 51481, updated on 11-Jun-2021

Summary

Official Symbol
VCX3Aprovided by HGNC
Official Full Name
variable charge X-linked 3Aprovided by HGNC
Primary source
HGNC:HGNC:18159
See related
Ensembl:ENSG00000169059 MIM:300533
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
VCX3; VCXA; VCX-A; VCX8R; VCX-8r
Summary
This gene belongs to the VCX/Y gene family, which has multiple members on both X and Y chromosomes, and all are expressed exclusively in male germ cells. The X-linked members are clustered on chromosome Xp22 and Y-linked members are two identical copies of the gene within a palindromic region on Yq11. The family members share a high degree of sequence identity, with the exception that a 30-bp unit is tandemly repeated in X-linked members but occurs only once in Y-linked members. The VCX gene cluster is polymorphic in terms of copy number; different individuals may have a different number of VCX genes. VCX/Y genes encode small and highly charged proteins of unknown function. The presence of a putative bipartite nuclear localization signal suggests that VCX/Y members are nuclear proteins. This gene contains 8 repeats of the 30-bp unit. [provided by RefSeq, Jul 2008]
Expression
Restricted expression toward testis (RPKM 27.7) See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See VCX3A in Genome Data Viewer
Location:
Xp22.31
Exon count:
3
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (6533618..6535118, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (6451659..6453159, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene microRNA 4770 Neighboring gene RPS5 pseudogene 8 Neighboring gene S232-VCX3A recombination region Neighboring gene pseudouridine 5'-phosphatase Neighboring gene uncharacterized LOC107987331 Neighboring gene RPS27A pseudogene 17

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Phenotypes

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated 2012-10-12)

ClinGen Genome Curation Page
Triplosensitivity

Dosage sensitivity unlikely (Last evaluated 2012-10-12)

ClinGen Genome Curation Page

General gene information

Markers

Homology

Clone Names

  • MGC118976, MGC125730, MGC125796

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in brain development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in brain development IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in nucleolus ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
variable charge X-linked protein 3
Names
variable charge protein on X with eight repeats
variably charged X-A
variably charged protein X-A

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011539.1 RefSeqGene

    Range
    5001..6501
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_016379.4NP_057463.2  variable charge X-linked protein 3

    See identical proteins and their annotated locations for NP_057463.2

    Status: REVIEWED

    Source sequence(s)
    AC108684, AF167078, BC039722
    Consensus CDS
    CCDS35199.1
    UniProtKB/Swiss-Prot
    Q9NNX9
    Related
    ENSP00000370479.3, ENST00000381089.7
    Conserved Domains (1) summary
    pfam15231
    Location:1141
    VCX_VCY; Variable charge X/Y family

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    6533618..6535118 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Support Center